Publications & Media#

Papers and preprints#

Neuroinformatics Unit publications#

Sirmpilatze, N., Felder, A., Abdulazhanova, D., Schwigon, L., Tatarnikov, I., Haase, K., Musielak, I., Kobylkov, D., Margrie, T. W., Mouritsen, H., Heyers, D., Tyson, A. L., Weiler, S. (2026) “An open-source three-dimensional digital brain atlas of a migratory bird, the Eurasian blackcap” Current Biology 2025.03.04.641293, doi.org/10.1016/j.cub.2026.03.034

https://doi.org/10.1016/j.cub.2026.03.034

Felder, A., Chapuis, G., Tatarnikov, I., Sirmpilatze, N., Tyson, A. (2026). Mapping the state of neuroscientific software - a vision for collaboration beyond single institutes or labs (1.0). Zenodo, doi.org/10.5281/zenodo.19945701

https://doi.org/10.5281/zenodo.19945701

Duporge, I., Minano, S., Sirmpilatze, N., Tatarnikov, I., Wolf, S., Tyson, A. L., Rubenstein, D. (2025) “Tracking the Flight: Exploring a Computational Framework for Analyzing Escape Responses in Plains Zebra (Equus quagga)” arXiv 2505.16882, doi.org/10.48550/arXiv.2505.16882

https://doi.org/10.48550/arXiv.2505.16882

Domine, C. C. J., Carrasco-Davis, R., Hollingsworth L., Sirmpilatze, N., Tyson, A. L., Jarvis, D., Barry, C., Saxe, A. M. (2024) “NeuralPlayground: A Standardised Environment for Evaluating Models of Hippocampus and Entorhinal Cortex” bioRxiv, doi.org/10.1101/2024.03.06.583699

https://doi.org/10.1101/2024.03.06.583699

Publications relating to Neuroinformatics Unit software#

Tyson, A. L., Vélez-Fort, M., Rousseau, C. V., Cossell, L., Tsitoura, C., Lenzi, S. C., Obenhaus, H. A., Claudi, F., Branco, T., Margrie, T. W. (2022) “Accurate determination of marker location within whole-brain microscopy images” Scientific Reports, doi.org/10.1038/s41598-021-04676-9

https://doi.org/10.1038/s41598-021-04676-9

Tyson, A. L., Rousseau, C. V., Niedworok, C. J., Keshavarzi, S., Tsitoura, C., Cossell, L., Strom, M., Margrie, T. W. (2021) “A deep learning algorithm for 3D cell detection in whole mouse brain image datasets” PLOS Computational Biology 17(5): e1009074, doi.org/10.1371/journal.pcbi.1009074

https://doi.org/10.1371/journal.pcbi.1009074

Claudi, F., Tyson, A. L., Petrucco, L., Margrie, T.W., Portugues, R., Branco, T. (2021) “Visualizing anatomically registered data with Brainrender” eLife 2021;10:e65751 doi.org/10.7554/eLife.65751

https://doi.org/10.7554/eLife.65751

Claudi, F., Petrucco, L., Tyson, A. L., Branco, T., Margrie, T. W., Portugues, R. (2020) “BrainGlobe Atlas API: a common interface for neuroanatomical atlases” Journal of Open Source Software 5(54), 2668 doi.org/10.21105/joss.02668

https://doi.org/10.21105/joss.02668